Package htsjdk.samtools
Class BAMIndexMetaData
java.lang.Object
htsjdk.samtools.BAMIndexMetaData
Metadata about the bam index contained within the bam index.
One instance created per index file.
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Method Summary
Modifier and TypeMethodDescriptionint
static BAMIndexMetaData[]
Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinateint
static void
printIndexStats
(File inputBamFile) Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate
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Method Details
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getAlignedRecordCount
public int getAlignedRecordCount()- Returns:
- the count of aligned records associated with this reference
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getUnalignedRecordCount
public int getUnalignedRecordCount()- Returns:
- the count of unaligned records associated with this reference
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printIndexStats
Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate -
getIndexStats
Prints meta-data statistics from BAM index (.bai or .csi) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate
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